A major need in immunogenetic studies are fast, reproducible and sensitive methods for amino acid sequence analysis of proteins. Mass spectrometric (MS) techniques provide a promising means of meeting these goals. One method utilizing MS presently under study involves enzymatic digestion of polypeptides into dipeptides using Dipeptidyl Aminopeptidase (DAP method). Another employs direct introduction (DI) of derivatized peptides for analysis. Computer assisted data analysis programs for both MS methods are also under development. The DAP and DI methods are being tested using rabbit heavy chains as model proteins because these proteins are not readily amenable to routine sequence analysis techniques. A further advantage of H chains is that they have regions of known constant sequences that are useful as controls on the new methodology.